Starting phenix.real_space_refine on Tue Feb 11 21:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.map" model { file = "/net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spb_40678/02_2025/8spb_40678.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4264 2.51 5 N 1134 2.21 5 O 1278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6726 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "C" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Chain: "a" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1332 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 7, 'TRANS': 158} Chain: "b" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain: "c" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Time building chain proxies: 4.97, per 1000 atoms: 0.74 Number of scatterers: 6726 At special positions: 0 Unit cell: (72.21, 138.61, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1278 8.00 N 1134 7.00 C 4264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 900.1 milliseconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1596 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 16 sheets defined 22.2% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 110 through 119 removed outlier: 3.885A pdb=" N PHE A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 115 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 194 through 198 Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.597A pdb=" N PHE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.872A pdb=" N LYS A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 334 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'a' and resid 110 through 121 removed outlier: 3.520A pdb=" N CYS a 118 " --> pdb=" O PHE a 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS a 119 " --> pdb=" O LEU a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 154 through 169 Processing helix chain 'a' and resid 180 through 193 Processing helix chain 'a' and resid 194 through 200 removed outlier: 3.522A pdb=" N LYS a 198 " --> pdb=" O PRO a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 238 Processing helix chain 'a' and resid 243 through 247 Processing helix chain 'b' and resid 321 through 334 Processing helix chain 'b' and resid 338 through 350 Processing helix chain 'c' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.792A pdb=" N ALA A 138 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 204 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 203 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE A 254 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU A 205 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N GLN A 256 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 207 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 217 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 269 Processing sheet with id=AA4, first strand: chain 'B' and resid 291 through 294 Processing sheet with id=AA5, first strand: chain 'B' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.697A pdb=" N ALA C 162 " --> pdb=" O ILE C 173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.526A pdb=" N SER C 46 " --> pdb=" O MET C 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.954A pdb=" N ILE C 100 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 3.603A pdb=" N MET C 149 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 172 through 176 removed outlier: 3.832A pdb=" N ALA a 138 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU a 137 " --> pdb=" O PHE a 204 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL a 206 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU a 139 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET a 208 " --> pdb=" O LEU a 139 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE a 141 " --> pdb=" O MET a 208 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE b 301 " --> pdb=" O LYS a 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 215 through 217 Processing sheet with id=AB3, first strand: chain 'b' and resid 319 through 320 Processing sheet with id=AB4, first strand: chain 'c' and resid 18 through 19 removed outlier: 6.153A pdb=" N LEU c 23 " --> pdb=" O LEU c 172 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU c 172 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE c 25 " --> pdb=" O PHE c 170 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA c 162 " --> pdb=" O ILE c 173 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 45 through 46 removed outlier: 3.508A pdb=" N SER c 46 " --> pdb=" O MET c 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'c' and resid 84 through 88 removed outlier: 6.122A pdb=" N ILE c 100 " --> pdb=" O LEU c 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 84 through 88 removed outlier: 3.918A pdb=" N MET c 149 " --> pdb=" O VAL c 189 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL c 189 " --> pdb=" O MET c 149 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2190 1.34 - 1.46: 942 1.46 - 1.57: 3650 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6856 Sorted by residual: bond pdb=" N ILE C 11 " pdb=" CA ILE C 11 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N LYS a 249 " pdb=" CA LYS a 249 " ideal model delta sigma weight residual 1.453 1.487 -0.035 1.18e-02 7.18e+03 8.67e+00 bond pdb=" N LYS c 148 " pdb=" CA LYS c 148 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.21e+00 bond pdb=" N LYS C 148 " pdb=" CA LYS C 148 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.15e+00 bond pdb=" N ILE a 140 " pdb=" CA ILE a 140 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.28e-02 6.10e+03 6.49e+00 ... (remaining 6851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 9164 3.23 - 6.45: 56 6.45 - 9.68: 8 9.68 - 12.91: 0 12.91 - 16.14: 2 Bond angle restraints: 9230 Sorted by residual: angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" C ASN C 12 " ideal model delta sigma weight residual 108.17 124.31 -16.14 1.85e+00 2.92e-01 7.61e+01 angle pdb=" N ASN C 12 " pdb=" CA ASN C 12 " pdb=" CB ASN C 12 " ideal model delta sigma weight residual 110.46 101.21 9.25 1.42e+00 4.96e-01 4.24e+01 angle pdb=" N ILE C 11 " pdb=" CA ILE C 11 " pdb=" C ILE C 11 " ideal model delta sigma weight residual 109.34 122.27 -12.93 2.08e+00 2.31e-01 3.86e+01 angle pdb=" C ARG C 167 " pdb=" CA ARG C 167 " pdb=" CB ARG C 167 " ideal model delta sigma weight residual 117.23 110.34 6.89 1.36e+00 5.41e-01 2.57e+01 angle pdb=" C ARG c 167 " pdb=" CA ARG c 167 " pdb=" CB ARG c 167 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 ... (remaining 9225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3573 17.99 - 35.97: 465 35.97 - 53.96: 132 53.96 - 71.94: 17 71.94 - 89.93: 9 Dihedral angle restraints: 4196 sinusoidal: 1756 harmonic: 2440 Sorted by residual: dihedral pdb=" CA VAL c 47 " pdb=" C VAL c 47 " pdb=" N ILE c 48 " pdb=" CA ILE c 48 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA VAL C 47 " pdb=" C VAL C 47 " pdb=" N ILE C 48 " pdb=" CA ILE C 48 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR c 37 " pdb=" C TYR c 37 " pdb=" N PHE c 38 " pdb=" CA PHE c 38 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 4193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 818 0.055 - 0.109: 162 0.109 - 0.164: 30 0.164 - 0.218: 3 0.218 - 0.273: 3 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CA ASN C 12 " pdb=" N ASN C 12 " pdb=" C ASN C 12 " pdb=" CB ASN C 12 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA THR c 188 " pdb=" N THR c 188 " pdb=" C THR c 188 " pdb=" CB THR c 188 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE C 11 " pdb=" N ILE C 11 " pdb=" C ILE C 11 " pdb=" CB ILE C 11 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1013 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 307 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO b 308 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO b 308 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO b 308 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 124 " 0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO C 125 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 125 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 125 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 37 " 0.007 2.00e-02 2.50e+03 1.20e-02 2.88e+00 pdb=" CG TYR c 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR c 37 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR c 37 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR c 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR c 37 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 37 " 0.000 2.00e-02 2.50e+03 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 985 2.76 - 3.30: 6429 3.30 - 3.83: 10700 3.83 - 4.37: 12308 4.37 - 4.90: 21335 Nonbonded interactions: 51757 Sorted by model distance: nonbonded pdb=" N GLU C 31 " pdb=" OE1 GLU C 31 " model vdw 2.227 3.120 nonbonded pdb=" OG SER c 86 " pdb=" OG1 THR c 99 " model vdw 2.237 3.040 nonbonded pdb=" OG SER C 86 " pdb=" OG1 THR C 99 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 135 " pdb=" OG1 THR A 135 " model vdw 2.268 3.040 nonbonded pdb=" O PHE B 330 " pdb=" OG SER B 334 " model vdw 2.278 3.040 ... (remaining 51752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.400 Set scattering table: 0.000 Process input model: 19.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6856 Z= 0.207 Angle : 0.731 16.137 9230 Z= 0.430 Chirality : 0.047 0.273 1016 Planarity : 0.004 0.066 1192 Dihedral : 17.299 89.931 2600 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.18 % Allowed : 25.79 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.28), residues: 812 helix: 0.53 (0.41), residues: 148 sheet: -0.38 (0.42), residues: 160 loop : -1.61 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.017 0.001 PHE c 170 TYR 0.028 0.001 TYR c 37 ARG 0.003 0.000 ARG c 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.910 Fit side-chains REVERT: C 138 PHE cc_start: 0.6988 (m-80) cc_final: 0.6609 (m-80) REVERT: C 152 GLU cc_start: 0.3870 (tp30) cc_final: 0.3668 (tp30) REVERT: a 182 ARG cc_start: 0.8132 (mmp80) cc_final: 0.7921 (mmt180) REVERT: c 103 LYS cc_start: 0.5659 (tttt) cc_final: 0.5165 (tttp) outliers start: 9 outliers final: 4 residues processed: 244 average time/residue: 0.2173 time to fit residues: 68.0208 Evaluate side-chains 218 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 214 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain c residue 119 PHE Chi-restraints excluded: chain c residue 160 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 0.0040 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN C 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123059 restraints weight = 7207.329| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.33 r_work: 0.3269 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6856 Z= 0.272 Angle : 0.596 7.197 9230 Z= 0.320 Chirality : 0.043 0.152 1016 Planarity : 0.004 0.045 1192 Dihedral : 6.025 56.032 899 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.00 % Allowed : 26.18 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.28), residues: 812 helix: 0.81 (0.39), residues: 152 sheet: -0.18 (0.42), residues: 160 loop : -1.58 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 335 HIS 0.003 0.001 HIS b 295 PHE 0.021 0.001 PHE C 13 TYR 0.018 0.001 TYR c 37 ARG 0.002 0.000 ARG a 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.773 Fit side-chains REVERT: B 373 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8237 (mm) REVERT: C 31 GLU cc_start: 0.8199 (pm20) cc_final: 0.7996 (pm20) REVERT: C 45 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7816 (pp) REVERT: C 123 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7478 (m110) REVERT: a 223 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7804 (pm20) outliers start: 38 outliers final: 20 residues processed: 235 average time/residue: 0.1878 time to fit residues: 58.1949 Evaluate side-chains 224 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 342 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 26 ILE Chi-restraints excluded: chain c residue 104 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN b 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.192471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121807 restraints weight = 7362.934| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.36 r_work: 0.3241 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6856 Z= 0.277 Angle : 0.599 8.687 9230 Z= 0.316 Chirality : 0.043 0.143 1016 Planarity : 0.004 0.039 1192 Dihedral : 5.403 48.717 895 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.26 % Allowed : 26.71 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 812 helix: 0.75 (0.39), residues: 154 sheet: -0.31 (0.42), residues: 164 loop : -1.61 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 335 HIS 0.003 0.001 HIS B 309 PHE 0.016 0.001 PHE C 13 TYR 0.012 0.001 TYR c 159 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 0.756 Fit side-chains REVERT: B 373 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8280 (mm) REVERT: C 45 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7894 (pp) REVERT: a 201 ASP cc_start: 0.9037 (p0) cc_final: 0.8835 (p0) REVERT: a 223 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7914 (pm20) REVERT: c 165 LYS cc_start: 0.7375 (tptt) cc_final: 0.7126 (ttmm) REVERT: c 168 ASP cc_start: 0.7142 (t0) cc_final: 0.6900 (t0) outliers start: 40 outliers final: 30 residues processed: 228 average time/residue: 0.2008 time to fit residues: 59.0442 Evaluate side-chains 242 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 341 GLU Chi-restraints excluded: chain b residue 342 VAL Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 112 CYS Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 0.0170 chunk 27 optimal weight: 0.0980 chunk 36 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123682 restraints weight = 7411.521| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.36 r_work: 0.3266 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6856 Z= 0.225 Angle : 0.580 7.740 9230 Z= 0.305 Chirality : 0.043 0.140 1016 Planarity : 0.003 0.036 1192 Dihedral : 5.211 45.130 895 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.66 % Allowed : 26.84 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.28), residues: 812 helix: 0.97 (0.40), residues: 154 sheet: -0.45 (0.41), residues: 164 loop : -1.64 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.013 0.001 PHE C 13 TYR 0.028 0.001 TYR c 37 ARG 0.003 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.738 Fit side-chains REVERT: B 314 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.5989 (ttp80) REVERT: B 373 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8263 (mm) REVERT: C 31 GLU cc_start: 0.8204 (pm20) cc_final: 0.7992 (pm20) REVERT: C 45 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7875 (pp) REVERT: C 123 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7496 (m110) REVERT: C 184 SER cc_start: 0.4665 (m) cc_final: 0.4108 (t) REVERT: a 201 ASP cc_start: 0.9067 (p0) cc_final: 0.8860 (p0) REVERT: a 223 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7927 (pm20) REVERT: a 227 ASP cc_start: 0.8125 (t70) cc_final: 0.7889 (t0) REVERT: b 373 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8533 (mm) outliers start: 43 outliers final: 29 residues processed: 232 average time/residue: 0.1932 time to fit residues: 58.8362 Evaluate side-chains 243 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 373 LEU Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 104 CYS Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 0.3980 chunk 42 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.195152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125076 restraints weight = 7326.841| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.36 r_work: 0.3285 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6856 Z= 0.194 Angle : 0.588 9.580 9230 Z= 0.304 Chirality : 0.042 0.136 1016 Planarity : 0.003 0.033 1192 Dihedral : 4.722 44.728 892 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.39 % Allowed : 27.50 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.28), residues: 812 helix: 1.03 (0.39), residues: 154 sheet: -0.63 (0.40), residues: 170 loop : -1.64 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 335 HIS 0.004 0.001 HIS B 338 PHE 0.011 0.001 PHE C 13 TYR 0.018 0.001 TYR c 37 ARG 0.006 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.819 Fit side-chains REVERT: A 227 ASP cc_start: 0.7993 (t0) cc_final: 0.7648 (t0) REVERT: B 314 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.5977 (ttp80) REVERT: B 373 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8279 (mm) REVERT: C 192 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7862 (mm-30) REVERT: a 123 GLU cc_start: 0.8598 (pm20) cc_final: 0.8309 (pm20) REVERT: a 157 PHE cc_start: 0.8206 (m-80) cc_final: 0.7846 (m-80) REVERT: a 201 ASP cc_start: 0.9044 (p0) cc_final: 0.8814 (p0) REVERT: a 223 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7909 (pm20) REVERT: a 227 ASP cc_start: 0.8106 (t70) cc_final: 0.7770 (t0) REVERT: b 318 MET cc_start: 0.8627 (mtp) cc_final: 0.8419 (mtt) REVERT: c 165 LYS cc_start: 0.7359 (tptt) cc_final: 0.7070 (ttmm) REVERT: c 166 GLU cc_start: 0.7090 (mp0) cc_final: 0.6769 (mp0) REVERT: c 168 ASP cc_start: 0.7177 (t0) cc_final: 0.6929 (t0) outliers start: 41 outliers final: 29 residues processed: 236 average time/residue: 0.1966 time to fit residues: 60.4210 Evaluate side-chains 245 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 310 ASN C 12 ASN C 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114989 restraints weight = 7393.061| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.29 r_work: 0.3166 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 6856 Z= 0.503 Angle : 0.713 7.368 9230 Z= 0.379 Chirality : 0.047 0.148 1016 Planarity : 0.004 0.042 1192 Dihedral : 5.512 47.718 892 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.51 % Favored : 92.36 % Rotamer: Outliers : 5.66 % Allowed : 28.16 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.27), residues: 812 helix: 0.29 (0.38), residues: 154 sheet: -1.03 (0.40), residues: 168 loop : -1.72 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP b 335 HIS 0.005 0.002 HIS A 221 PHE 0.015 0.002 PHE c 13 TYR 0.024 0.002 TYR c 37 ARG 0.004 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.759 Fit side-chains REVERT: A 223 GLU cc_start: 0.8339 (mp0) cc_final: 0.8068 (pm20) REVERT: A 227 ASP cc_start: 0.8297 (t0) cc_final: 0.7816 (t0) REVERT: B 373 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8389 (mm) REVERT: C 192 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8008 (mm-30) REVERT: a 124 GLU cc_start: 0.8364 (mp0) cc_final: 0.8072 (mp0) REVERT: a 201 ASP cc_start: 0.9079 (p0) cc_final: 0.8862 (p0) REVERT: a 223 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8203 (pm20) REVERT: a 227 ASP cc_start: 0.8186 (t70) cc_final: 0.7941 (t0) REVERT: b 293 LYS cc_start: 0.8297 (mttt) cc_final: 0.8095 (mttt) REVERT: c 106 LYS cc_start: 0.3227 (mttt) cc_final: 0.2968 (mmtt) outliers start: 43 outliers final: 34 residues processed: 238 average time/residue: 0.1922 time to fit residues: 59.7755 Evaluate side-chains 247 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 38 PHE Chi-restraints excluded: chain c residue 46 SER Chi-restraints excluded: chain c residue 52 ASN Chi-restraints excluded: chain c residue 99 THR Chi-restraints excluded: chain c residue 116 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 6 optimal weight: 0.0050 chunk 58 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 310 ASN ** b 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.191906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.121319 restraints weight = 7294.005| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.34 r_work: 0.3256 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6856 Z= 0.221 Angle : 0.633 8.141 9230 Z= 0.329 Chirality : 0.043 0.142 1016 Planarity : 0.003 0.035 1192 Dihedral : 5.035 45.640 892 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 4.34 % Allowed : 28.95 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.27), residues: 812 helix: 0.67 (0.38), residues: 154 sheet: -0.88 (0.41), residues: 164 loop : -1.69 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 335 HIS 0.004 0.001 HIS B 338 PHE 0.010 0.001 PHE C 13 TYR 0.020 0.001 TYR c 37 ARG 0.007 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.813 Fit side-chains REVERT: A 123 GLU cc_start: 0.8932 (pm20) cc_final: 0.8698 (pm20) REVERT: A 227 ASP cc_start: 0.8045 (t70) cc_final: 0.7559 (t0) REVERT: B 373 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8384 (mm) REVERT: C 122 MET cc_start: 0.7713 (mmt) cc_final: 0.6995 (tpt) REVERT: C 192 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7944 (mm-30) REVERT: a 123 GLU cc_start: 0.8568 (pm20) cc_final: 0.8332 (pm20) REVERT: a 201 ASP cc_start: 0.9042 (p0) cc_final: 0.8812 (p0) REVERT: a 223 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8177 (pm20) REVERT: a 227 ASP cc_start: 0.8079 (t70) cc_final: 0.7823 (t0) outliers start: 33 outliers final: 26 residues processed: 222 average time/residue: 0.1970 time to fit residues: 57.2171 Evaluate side-chains 234 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.192744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.122422 restraints weight = 7318.669| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.29 r_work: 0.3276 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6856 Z= 0.227 Angle : 0.634 9.030 9230 Z= 0.326 Chirality : 0.043 0.144 1016 Planarity : 0.003 0.035 1192 Dihedral : 4.969 46.137 892 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.53 % Favored : 93.35 % Rotamer: Outliers : 4.47 % Allowed : 28.55 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.28), residues: 812 helix: 0.82 (0.38), residues: 154 sheet: -0.92 (0.40), residues: 170 loop : -1.69 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.009 0.001 PHE c 13 TYR 0.021 0.001 TYR c 37 ARG 0.006 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.803 Fit side-chains REVERT: A 123 GLU cc_start: 0.8932 (pm20) cc_final: 0.8701 (pm20) REVERT: A 227 ASP cc_start: 0.8079 (t70) cc_final: 0.7673 (t0) REVERT: B 373 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8322 (mm) REVERT: C 121 GLU cc_start: 0.6691 (pt0) cc_final: 0.6488 (pt0) REVERT: C 122 MET cc_start: 0.7755 (mmt) cc_final: 0.7056 (tpt) REVERT: C 192 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7945 (mm-30) REVERT: a 123 GLU cc_start: 0.8589 (pm20) cc_final: 0.8329 (pm20) REVERT: a 201 ASP cc_start: 0.9000 (p0) cc_final: 0.8763 (p0) REVERT: a 223 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8178 (pm20) REVERT: a 227 ASP cc_start: 0.8137 (t70) cc_final: 0.7917 (t0) outliers start: 34 outliers final: 27 residues processed: 222 average time/residue: 0.1982 time to fit residues: 57.3830 Evaluate side-chains 234 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 202 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 16 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 310 ASN ** b 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.196545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126344 restraints weight = 7314.077| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.32 r_work: 0.3326 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6856 Z= 0.180 Angle : 0.622 8.926 9230 Z= 0.319 Chirality : 0.042 0.143 1016 Planarity : 0.003 0.032 1192 Dihedral : 4.770 44.164 892 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 3.55 % Allowed : 29.08 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 812 helix: 1.07 (0.39), residues: 154 sheet: -0.67 (0.42), residues: 162 loop : -1.60 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.010 0.001 PHE c 13 TYR 0.019 0.001 TYR c 37 ARG 0.007 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.7929 (t70) cc_final: 0.7398 (t0) REVERT: B 373 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 122 MET cc_start: 0.7832 (mmt) cc_final: 0.7396 (tpt) REVERT: a 123 GLU cc_start: 0.8581 (pm20) cc_final: 0.8329 (pm20) REVERT: a 157 PHE cc_start: 0.8245 (m-80) cc_final: 0.7978 (m-80) REVERT: a 201 ASP cc_start: 0.8967 (p0) cc_final: 0.8748 (p0) REVERT: a 223 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8089 (mp0) REVERT: a 227 ASP cc_start: 0.8170 (t70) cc_final: 0.7947 (t0) REVERT: c 31 GLU cc_start: 0.8578 (pm20) cc_final: 0.8370 (pm20) REVERT: c 87 MET cc_start: 0.5409 (pmm) cc_final: 0.4434 (ppp) outliers start: 27 outliers final: 25 residues processed: 213 average time/residue: 0.1991 time to fit residues: 55.6104 Evaluate side-chains 220 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 123 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.195026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.125103 restraints weight = 7456.319| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.30 r_work: 0.3305 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6856 Z= 0.214 Angle : 0.640 8.854 9230 Z= 0.331 Chirality : 0.043 0.147 1016 Planarity : 0.003 0.034 1192 Dihedral : 4.832 44.330 892 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.28 % Favored : 93.60 % Rotamer: Outliers : 3.95 % Allowed : 29.87 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.28), residues: 812 helix: 1.00 (0.39), residues: 154 sheet: -0.63 (0.42), residues: 162 loop : -1.58 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 335 HIS 0.003 0.001 HIS A 148 PHE 0.012 0.001 PHE c 13 TYR 0.034 0.001 TYR c 37 ARG 0.007 0.000 ARG C 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 227 ASP cc_start: 0.8150 (t70) cc_final: 0.7756 (t0) REVERT: B 373 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8327 (mm) REVERT: C 122 MET cc_start: 0.7817 (mmt) cc_final: 0.7395 (tpt) REVERT: a 123 GLU cc_start: 0.8617 (pm20) cc_final: 0.8359 (pm20) REVERT: a 157 PHE cc_start: 0.8230 (m-80) cc_final: 0.7953 (m-80) REVERT: a 201 ASP cc_start: 0.8972 (p0) cc_final: 0.8749 (p0) REVERT: a 223 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8084 (pm20) REVERT: a 227 ASP cc_start: 0.8203 (t70) cc_final: 0.7989 (t0) REVERT: c 87 MET cc_start: 0.5518 (pmm) cc_final: 0.4572 (ppp) outliers start: 30 outliers final: 27 residues processed: 213 average time/residue: 0.1911 time to fit residues: 53.5168 Evaluate side-chains 230 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 148 LYS Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain a residue 156 ASP Chi-restraints excluded: chain a residue 186 SER Chi-restraints excluded: chain a residue 228 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 236 GLN Chi-restraints excluded: chain a residue 268 VAL Chi-restraints excluded: chain b residue 312 SER Chi-restraints excluded: chain b residue 340 GLU Chi-restraints excluded: chain b residue 349 SER Chi-restraints excluded: chain b residue 368 THR Chi-restraints excluded: chain c residue 19 ILE Chi-restraints excluded: chain c residue 52 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.193483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123526 restraints weight = 7315.106| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.25 r_work: 0.3287 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6856 Z= 0.239 Angle : 0.653 8.695 9230 Z= 0.338 Chirality : 0.043 0.147 1016 Planarity : 0.003 0.035 1192 Dihedral : 4.909 45.494 892 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.53 % Favored : 93.35 % Rotamer: Outliers : 4.34 % Allowed : 29.87 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 812 helix: 0.91 (0.39), residues: 154 sheet: -0.75 (0.41), residues: 170 loop : -1.60 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP b 335 HIS 0.003 0.001 HIS B 295 PHE 0.012 0.001 PHE c 13 TYR 0.032 0.001 TYR c 37 ARG 0.007 0.000 ARG C 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4529.98 seconds wall clock time: 81 minutes 9.86 seconds (4869.86 seconds total)